Abstract 5168: Assessment and prognostic implication of 3-gene signature identified as potential biomarker in bladder cancer
Authors: Shiv Shankar Verma, Eswar Shankar, Spencer Lin, Vaibhav Singh, E. Ricky Chan, Shufen Cao, Gregory T MacLennan, Lee E. Ponsky, Sanjay Gupta
Journal: Cancer Research (2022)

Abstract The majority of bladder cancers present with non-muscle invasive disease (NIMBC) confined to the superficial layers of the bladder wall, however, 50-70% of patients will subsequently progress to muscle-invasive bladder cancer (MIBC) that will require more aggressive treatment. For patient stratification, the current prognostication relies on tumor stage and grade, which remains challenging due to the lack of appropriate biomarker(s) to monitor disease progress. Therefore, there is an urgent need for predictive biomarkers that can distinguish between progressive versus non-progressive disease for the identification of patients to better stratify their risk of progression. Here we aim to identify novel prognostic biomarker(s) associated with disease progression by exploring bladder cancer patient gene expression database. We explored and analyzed the transcriptomic gene expression of bladder cancer patient datasets consisting of NIMBC and MIBC subtype from the NCBI GEO (GSE154261, GSE57813, and GSE37317) database. These datasets were analyzed using GEO2R (an R-based web application) and Limma R packages. Pathway enrichment analysis of differentially expressed genes (DEGs) between the NMIBC and MIBC group was analyzed using the ingenuity pathway analysis (IPA), metascape web-based portal, and Cytoscape. The above finding was functionally validated in human bladder cancer cell lines; RT4 (transitional cell papilloma), J82 (transitional cell carcinoma), HT1197 (bladder carcinoma), and 253JB-V (metastatic phenotype) and compared with the relative expression ofUROtsa (benign) urothelial cell line. A total of 1516 DEGs were identified between non-muscle-invasive and muscle-invasive bladder cancer specimens. To identify genes of prognostic value, we performed Gene Ontology (GO) and Kyoto Gene and Genomic encyclopedia (KEGG)analysis. A total of seven genes including CDKN2A, CDC20, CTSV, FOXM1, MAGEA6, KRT23, and S100A9 were confirmed with strong prognostic values in bladder cancer and validated by qRT-PCR conducted in various human bladder cancer cells representing stage-specific disease progression. ULCAN, human protein atlas, and The Cancer Genome Atlas datasets were used to confirm the predictive value of these genes in bladder cancer progression. Moreover, Kaplan-Meier analysis and Cox-hazard ratio analysis were performed to determine the prognostic role of these genes. Univariate analysis performed on a validation set identified a 3-panel gene set viz. CDKN2A, CTSV and FOXM1 with 95.5% sensitivity and 100% specificity in predicting bladder cancer progression. Our study screened and confirmed a panel of a 3-genes biomarkers that could precisely predict the progression and prognosis of bladder cancer. Citation Format: Shiv Shankar Verma, Eswar Shankar, Spencer Lin, Vaibhav Singh, E. Ricky Chan, Shufen Cao, Gregory T MacLennan, Lee E. Ponsky, Sanjay Gupta. Assessment and prognostic implication of 3-gene signature identified as potential biomarker in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5168.